According to figures from the Department for Children, Schools and Families, 6.26 per cent of morning and afternoon sessions were missed – with or without an excuse – during the autumn term, compared with 5.94 per cent a year earlier.

The truancy rate – days missed without permission – jumped from 0.9 per cent to 0.94 per cent, meaning almost 60,000 pupils bunked off every day. Officials identified 43,920 "persistent absentees" who missed almost half of all school days during the four-month period.

A further 305,030 pupils, who each missed one lesson in five, were judged to be at risk of joining the problem group.

The Government admitted that pupils persistently missing school represented a "major challenge we must tackle".

Kevin Brennan, the children's minister, insisted that fewer secondary school pupils missed classes than in 2006.

"The reduction of overall absence and persistent absenteeism in secondary schools shows that our policies are working," he said.

"The emerging evidence shows the rise in absence in primary schools last autumn was largely due to illness."

Christine Blower, the acting general secretary of the National Union of Teachers, said the Government had to "draw the obvious lessons" from the latest figures.

Schools needed "the freedom to make the curriculum as flexible as possible in order to engage school refusers", she said.

About £1 billion has been spent on strategies to improve attendance and poor behaviour since 1997.

They include penalty fines for parents, town centre truancy sweeps and text message alerts to parents.

Last week, it emerged that an increase in the number of £50 fines handed out to parents had done little to cut truancy rates.

Ministers have been forced to scale back targets for tackling truancy and have dropped national targets for reducing unauthorised absence altogether.

David Laws, the Liberal Democrats' children's spokesman, said: "Parents have a duty to ensure that their children attend school, but this increase in persistent truancy shows that the Government's strategy to tackle this problem is failing."